If you want to stay in the Toshima district of Tokyo, Ikebukuro Sugamo 202 Apartment Tokyo is a good choice located, nearly a 25-minute walk from the Koishikawa Botanical Gardens.
The National Museum of Nature and Science can be reached by car in a few minutes, while the Sugamo Otori Shrine is right by this apartment. The Baseball Hall of Fame and Museum is around 3 km from the apartment, and Tokyo International airport is less than a 30-minute drive away.
The nearest tube station is Sengoku, which is approximately 5 minutes' walk away.